% Generated by roxygen2: do not edit by hand

% Please edit documentation in R/face_mask.R

\name{ct_face_mask}

\alias{ct_face_mask}

\alias{ct_face_mask,mri_face_mask}

\alias{mri_face_mask}

\title{Create Mask of the Face}

\usage{

ct_face_mask(

  file,

  skull_strip = TRUE,

  mask = NULL,

  robust = TRUE,

  template.file = system.file(ifelse(skull_strip, "scct_unsmooth_SS_0.01.nii.gz",

    "scct_unsmooth.nii.gz"), package = "ichseg"),

  template.face_mask = NULL,

  template.face_mask_inds = list(50:130, 170:217, 1:15),

  extend_mask = TRUE,

  typeofTransform = "Affine",

  swapdim = TRUE,

  verbose = TRUE,

  ...

)

mri_face_mask(

  ...,

  skull_strip = TRUE,

  mask = NULL,

  robust = FALSE,

  template.file = mni_fname(brain = skull_strip)

)

}

\arguments{

\item{file}{File for face masking - either filename or class nifti}

\item{skull_strip}{Should the data require skull stripping if

no mask is provided?}

\item{mask}{file or \code{nifti} to mask the \code{file}}

\item{robust}{If \code{mask = NULL}, then \code{robust} is

passed to \code{\link{CT_Skull_Stripper}}}

\item{template.file}{Template to warp to original image space}

\item{template.face_mask}{Mask of template to use as rough face mask.  If

\code{template.file} is not specified, \code{template.face_mask_inds}

must be}

\item{template.face_mask_inds}{List of length 3 for indices of

\code{template.file} to indicate the mask.}

\item{extend_mask}{after transformation, should the mask be extended to the

front of the image to ensure all face has been removed?}

\item{typeofTransform}{Transformation for template to image, passed to

\code{\link{ants_regwrite}}.}

\item{swapdim}{Should the dimensions be swapped before registration,

and then reset after}

\item{verbose}{Print out diagnostic messages}

\item{...}{arguments passed to \code{\link{CT_Skull_Stripper}}}

}

\value{

Object of class nifti

}

\description{

Creates a rough mask of the face from a head scan

}

\examples{

\dontrun{

file = "~/Desktop/Desktop/scratch/100-318_20070723_0957_CT_3_CT_Head-.nii.gz"

mask = NULL

robust = FALSE

face = ct_face_mask(

   file = file,

   robust = FALSE

   )

 img = readnii(file)

 rimg = randomize_mask(img, mask = face)

}

\dontrun{

library(fslr)

library(extrantsr)

mri = "~/Desktop/Desktop/scratch/SUBJ0001-01-MPRAGE.nii.gz"

template.file = mni_fname(brain = TRUE)

tmask = mni_fname(brain = TRUE, mask = TRUE)

template.face_mask_inds = list(50:130, 170:217, 1:15)

brain = fslbet_robust(mri,

remove.neck = TRUE,

remover = "double_remove_neck",

template.file = template.file,

template.mask = tmask)

mask = brain > 0

img = brain

template.face_mask = NULL

verbose = TRUE

face = mri_face_mask(

   file = img,

   mask = mask,

   template.file = template.file

   )

}

}